Functional

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The Matlab software interface we use for analyzing functional and anatomical data mrVista, is pronounced mister-Vista. The MR stands for magnetic resonance and the VISTA refers to the VISTALAB name (vision, image science, and technology applications) that the Wandell lab has used for more than 15 years.

Elsewhere in this manual you can find a primer on functional MRI.

[edit] Functional-MR Page Jump

[edit] Introduction

MrVista offers several ways to interact with functional and anatomical data.

  • Inplane views represent the data in the format that comes out of the scanner, overlaying maps computed off the functional images onto coregistered anatomical images;
  • Flat views represent the gray matter-restricted data as projected on to a 2-dimensional ("flattened") cortical surface.

MrVista is also an interface to a range of analysis methods. These include

The MR pulse sequence and data pre-processing methods are described in separate pages. They include a review of the spiral pulse sequences, SSFP methods, and pre-processing of the functional data. They also describe the pre-processing of the data, which involves reconstructing the time series images (reconning) and transferring the data from the Lucas Center to our lab computers.

The functional data are integrated with the diffusion imaging using the mrDiffusion tools developed by Bob Dougherty. He built those tools and also played a significant role in developing most of the MrVista tools.

[edit] References

There is an older tutorial of the interface for the psych 204 class.

(Minor footnote of interest to N < 10 people: Originally the Wandell and Heeger labs, including Engel, Boynton, Poirson, and others, developed the MR software together. After Dave Heeger went to the big Apple, his lab branched. Their Wiki page uses the classic name of the software, mrLoadRet. This was the name Steve Engel used, referring to magnetic resonance, load retinotopy data. Larsson, Schluppeck, Gardner, and others added to their tools. Whenever we visit, we say that we should merge things. I hope that happens some day.)

Spiral Pulse Sequences

  • Glover GH, Lai S., 1998. Self-navigated spiral fMRI: interleaved versus single-shot. Magn Reson Med. 1998 Mar;39(3):361-8.

PubMed

  • Lai S, Glover GH., 1998. Three-dimensional spiral fMRI technique: a comparison with 2D spiral acquisition. Magn Reson Med. 1998 Jan;39(1):68-78.

PubMed


Motion Compensation

  • Nestares O, Heeger DJ., 2000 Robust multiresolution alignment of MRI brain volumes. Magn Reson Med. 2000 May;43(5):705-15.

PubMed


Traveling Wave Analyses

  • Engel SA, Rumelhart DE, Wandell BA, Lee AT, Glover GH, Chichilnisky EJ, Shadlen MN., 1994. fMRI of human visual cortex. Nature. 1994 Jun 16;369(6481):525. PubMed

PDF


General Linear Model


Much Older VISTA lab manual

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